[R] data transformation

[Kingsford Jones]

Hi Christian,

Here's a way using the reshape package:

> dfr
   site lat lon spec1 spec2 spec3 spec4
1 site1  10  11     1     0     1     0
2 site2  20  21     1     1     1     0
3 site3  30  31     0     1     1     1
> library(reshape)
> dfr <- melt(dfr[, -1], id=1:2, variable_name='species')
> dfr <- dfr[dfr$value>0,]
> dfr
   lat lon species value
1   10  11   spec1     1
2   20  21   spec1     1
5   20  21   spec2     1
6   30  31   spec2     1
7   10  11   spec3     1
8   20  21   spec3     1
9   30  31   spec3     1
12  30  31   spec4     1


The 'value', variable is not interesting here, but if you had counts
rather than presence/absence it could be.

best,

Kingsford Jones

On Fri, May 2, 2008 at 2:27 PM, Christian Hof <chof at bio.ku.dk> wrote:
> Dear all,
>  how can I, with R, transform a presence-absence (0/1) matrix of species
> occurrences into a presence-only table (3 columns) with the names of the
> species (1st column), the lat information of the sites (2nd column) and the
> lon information of the sites (3rd column), as given in the below example?
>  Thanks a lot for your help!
>  Christian
>
>
>  my dataframe:
>
>  site    lat     lon     spec1   spec2   spec3   spec4
>  site1   10      11      1       0       1       0
>  site2   20      21      1       1       1       0
>  site3   30      31      0       1       1       1
>
>
>  my desired new dataframe:
>
>  species lat     lon
>  spec1   10      11
>  spec1   20      21
>  spec2   20      21
>  spec2   30      31
>  spec3   10      11
>  spec3   20      21
>  spec3   30      31
>  spec4   30      31
>
>
>
>  --
>  Christian Hof, PhD student
>
>  Center for Macroecology & Evolution
>  University of Copenhagen
>  www.macroecology.ku.dk
>  &
>  Biodiversity & Global Change Lab
>  Museo Nacional de Ciencias Naturales, Madrid
>  www.biochange-lab.eu
>
>  mobile ES .. +34 697 508 519
>  mobile DE .. +49 176 205 189 27
>      mail .. chof at bio.ku.dk
>     mail2 .. vogelwart at gmx.de
>      blog .. www.vogelwart.de
>
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